You pipe diameter is to big, you lost all the velocity of the exhaust. Once you loose the air speed, you loose the reversion and scavenging effects. Those tube sizes are big enough for a 500 inch engine. Use some of the calculators on line and be realistic with the rpm and air flow, and you should come up with some pretty good numbers.
I would think 1 5/8" for the single ports and 1 3/4" for the siamese ports. The siamese ports fire far enough apart that big diameter pipe is not needed. 2" would be maximum if you want to step it up.
How long did you make the primary pipes? 28" to 32" should be about right for under 5000 rpm, maybe a touch longer if the rpm is less. Shorter for higher rpm. Collectors should be 12" to 14" in length starting out. Watch for the bluing of the pipe or burning paint on the collector, thats the point at which you want to cut them or transition into exhaust pipes. 2 1/2" would be more then enough pipe diameter for collectors, 2 1/4" would also work. Three front ports into one, the other three into the second collector. Off setting collector length to even out the total header length shouldn't hurt it to bad if want then to end at the same spot.
Cross over tubes are not needed on 6 cylinder engines so connect the two pipes with a two in one out muffler or two separate pipes and mufflers. 2 1/4" is all you need for head pipe and tail pipe,
2 1/2" if running single pipe.
You main goal is to keep the exhaust hot so it keeps its speed. Large diameter pipe allows the gases to expand and cool, thus slowing them down. Its not just about getting the exhaust out of the engine, you also want it to work for you as it leaves. A really well designed header will create vacuum in the ports pulling fresh fuel and air into the cylinder at valve over lap increasing the efficiency of the engine which in turn makes more power.
